Merge tag 'upstream/6.1.20170106+dfsg1'.

Belatedly repackage without data/UniVec.*, some portions of which
turned out to be non-free (with copyright held by Invitrogen
Corporation, which requires a license for commercial use thereof.)

5 files changed, 71 insertions, 62 deletions

diff --git a/data/UniVec.nhr b/data/UniVec.nhr
deleted file mode 100644
index d00b6c46..00000000
--- a/data/UniVec.nhr
+++ /dev/null
diff --git a/data/UniVec.nin b/data/UniVec.nin
deleted file mode 100644
index 8a4bbcbc..00000000
--- a/data/UniVec.nin
+++ /dev/null
diff --git a/data/UniVec.nsq b/data/UniVec.nsq
deleted file mode 100644
index a57005bf..00000000
--- a/data/UniVec.nsq
+++ /dev/null
diff --git a/debian/changelog b/debian/changelog
index 85c50787..add95719 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+ncbi-tools6 (6.1.20170106+dfsg1-1) UNRELEASED; urgency=medium
+
+  * Belatedly repackage without data/UniVec.*, some portions of which
+    turned out to be non-free (with copyright held by Invitrogen
+    Corporation, which requires a license for commercial use thereof.)
+    (NOT RELEASED YET.)
+
+ -- Aaron M. Ucko <ucko@debian.org>  Sun, 28 Jul 2019 21:30:56 -0400
+
 ncbi-tools6 (6.1.20170106-7) unstable; urgency=medium
 
   [ Steffen Möller ]
diff --git a/debian/patches/debian-changes b/debian/patches/debian-changes
index f790ed02..3eb336f0 100644
--- a/debian/patches/debian-changes
+++ b/debian/patches/debian-changes
@@ -1,6 +1,6 @@
 Combined patches from git.
 --- /dev/null
-+++ ncbi-tools6-6.1.20170106/.gitignore
++++ ncbi-tools6-6.1.20170106+dfsg1/.gitignore
 @@ -0,0 +1,6 @@
 +bin
 +build
@@ -8,8 +8,8 @@ Combined patches from git.
 +lib
 +shlib
 +*-stamp
---- ncbi-tools6-6.1.20170106.orig/access/ent2api.c
-+++ ncbi-tools6-6.1.20170106/access/ent2api.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/access/ent2api.c
++++ ncbi-tools6-6.1.20170106+dfsg1/access/ent2api.c
 @@ -1273,7 +1273,7 @@ NLM_EXTERN CONN EntrezOpenConnection (
      *arg = '\0';
  
@@ -19,8 +19,8 @@ Combined patches from git.
  }
  
  #ifdef OS_MAC
---- ncbi-tools6-6.1.20170106.orig/api/sqnutil3.c
-+++ ncbi-tools6-6.1.20170106/api/sqnutil3.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/api/sqnutil3.c
++++ ncbi-tools6-6.1.20170106+dfsg1/api/sqnutil3.c
 @@ -33198,7 +33198,7 @@ ClickableItemPtr LIBCALL ClickableGlobal
         cip->clickable_item_type = item_type;
         cip->description 
@@ -30,8 +30,8 @@ Combined patches from git.
         return cip;
    }
    return NULL;
---- ncbi-tools6-6.1.20170106.orig/connect/ncbi_gnutls.c
-+++ ncbi-tools6-6.1.20170106/connect/ncbi_gnutls.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/ncbi_gnutls.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/ncbi_gnutls.c
 @@ -585,6 +585,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
  
      assert(!s_GnuTlsCredAnon);
@@ -48,8 +48,8 @@ Combined patches from git.
  
      val = ConnNetInfo_GetValue(0, "GNUTLS_LOGLEVEL", buf, sizeof(buf), 0);
      CORE_LOCK_READ;
---- ncbi-tools6-6.1.20170106.orig/connect/ncbi_http_connector.c
-+++ ncbi-tools6-6.1.20170106/connect/ncbi_http_connector.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/ncbi_http_connector.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/ncbi_http_connector.c
 @@ -240,8 +240,14 @@ static int/*bool*/ x_UnsafeRedirectOK(SH
      if (uuu->unsafe_redir == eDefault) {
          if (!(uuu->flags & fHTTP_UnsafeRedirects)) {
@@ -66,8 +66,8 @@ Combined patches from git.
              uuu->unsafe_redir = ConnNetInfo_Boolean(val) ? eOn : eOff;
          } else
              uuu->unsafe_redir = eOn;
---- ncbi-tools6-6.1.20170106.orig/connect/ncbi_util.c
-+++ ncbi-tools6-6.1.20170106/connect/ncbi_util.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/ncbi_util.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/ncbi_util.c
 @@ -49,7 +49,9 @@
  #  ifndef NCBI_OS_SOLARIS
  #    include <limits.h>
@@ -79,8 +79,8 @@ Combined patches from git.
  #    include <sys/user.h>
  #  endif /*NCBI_OS_LINUX*/
  #  include <pwd.h>
---- ncbi-tools6-6.1.20170106.orig/connect/urlquery.c
-+++ ncbi-tools6-6.1.20170106/connect/urlquery.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/urlquery.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/urlquery.c
 @@ -128,7 +128,10 @@ NLM_EXTERN CONN QUERY_OpenUrlQuery (
    }
    if ( host_port ) {
@@ -92,8 +92,8 @@ Combined patches from git.
    StringNCpy_0 (net_info->path, host_path, sizeof (net_info->path));
    if (StringDoesHaveText (arguments)) {
      StringNCpy_0 (net_info->args, arguments, sizeof (net_info->args));
---- ncbi-tools6-6.1.20170106.orig/corelib/ncbimain.c
-+++ ncbi-tools6-6.1.20170106/corelib/ncbimain.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/corelib/ncbimain.c
++++ ncbi-tools6-6.1.20170106+dfsg1/corelib/ncbimain.c
 @@ -67,6 +67,7 @@
  #pragma segment NlmSegA
  #endif
@@ -116,8 +116,8 @@ Combined patches from git.
  
    NlmThreadJoinAll();
  
---- ncbi-tools6-6.1.20170106.orig/corelib/ncbitime.c
-+++ ncbi-tools6-6.1.20170106/corelib/ncbitime.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/corelib/ncbitime.c
++++ ncbi-tools6-6.1.20170106+dfsg1/corelib/ncbitime.c
 @@ -77,6 +77,7 @@
  #include <ncbi.h>
  #include <ncbithr.h>
@@ -161,8 +161,8 @@ Combined patches from git.
    if ((dt = localtime (&ltime)) != NULL)
   	{
          Nlm_MemCopy ((Nlm_VoidPtr) dtp, (Nlm_VoidPtr) dt, sizeof (struct tm));
---- ncbi-tools6-6.1.20170106.orig/demo/asndisc.c
-+++ ncbi-tools6-6.1.20170106/demo/asndisc.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/asndisc.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/asndisc.c
 @@ -65,6 +65,7 @@
  #include <objmacro.h>
  #include <macroapi.h>
@@ -180,8 +180,8 @@ Combined patches from git.
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/entrez2.c
-+++ ncbi-tools6-6.1.20170106/demo/entrez2.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/entrez2.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/entrez2.c
 @@ -61,6 +61,8 @@
  
  #include <entrez2.h>
@@ -209,8 +209,8 @@ Combined patches from git.
    } else if (useTestServ) {
      EntrezSetService ("Entrez2Test");
    } else if (useURL) {
---- ncbi-tools6-6.1.20170106.orig/demo/findspl.c
-+++ ncbi-tools6-6.1.20170106/demo/findspl.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/findspl.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/findspl.c
 @@ -62,6 +62,8 @@
  #include <accentr.h>
  #include <sequtil.h>
@@ -229,8 +229,8 @@ Combined patches from git.
  	if ( !GetArgs("findspl", NUMARGS, myargs) ) return 1;
  
  	gi = myargs[0].intvalue;
---- ncbi-tools6-6.1.20170106.orig/demo/gbseqget.c
-+++ ncbi-tools6-6.1.20170106/demo/gbseqget.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/gbseqget.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/gbseqget.c
 @@ -54,6 +54,8 @@
  #include <pmfapi.h>
  #include <asn2gnbp.h>
@@ -249,8 +249,8 @@ Combined patches from git.
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/insdseqget.c
-+++ ncbi-tools6-6.1.20170106/demo/insdseqget.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/insdseqget.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/insdseqget.c
 @@ -55,6 +55,8 @@
  #include <pmfapi.h>
  #include <asn2gnbp.h>
@@ -269,8 +269,8 @@ Combined patches from git.
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/nps2gps.c
-+++ ncbi-tools6-6.1.20170106/demo/nps2gps.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/nps2gps.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/nps2gps.c
 @@ -50,6 +50,8 @@
  #include <toasn3.h>
  #include <pmfapi.h>
@@ -289,8 +289,8 @@ Combined patches from git.
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/taxblast_main.c
-+++ ncbi-tools6-6.1.20170106/demo/taxblast_main.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/taxblast_main.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/taxblast_main.c
 @@ -41,6 +41,8 @@ static char const rcsid[] = "$Id: taxbla
  #include <objgen.h>
  #include <taxblast.h>
@@ -309,8 +309,8 @@ Combined patches from git.
      if (!GetArgs("txblast", NUMARG, myargs)) {
          return 1;
      }
---- ncbi-tools6-6.1.20170106.orig/demo/tbl2asn.c
-+++ ncbi-tools6-6.1.20170106/demo/tbl2asn.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/tbl2asn.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/tbl2asn.c
 @@ -8911,10 +8911,12 @@ Int2 Main (void)
      return 1;
    }
@@ -334,8 +334,8 @@ Combined patches from git.
      return 1;
    }
  
---- ncbi-tools6-6.1.20170106.orig/desktop/bspview.c
-+++ ncbi-tools6-6.1.20170106/desktop/bspview.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/desktop/bspview.c
++++ ncbi-tools6-6.1.20170106+dfsg1/desktop/bspview.c
 @@ -2549,13 +2549,13 @@ NLM_EXTERN void Nlm_LaunchWebPage (Char
      }
  #endif
@@ -353,8 +353,8 @@ Combined patches from git.
          exit(-1);
      }
    }
---- ncbi-tools6-6.1.20170106.orig/doc/dispatcher.html
-+++ ncbi-tools6-6.1.20170106/doc/dispatcher.html
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/dispatcher.html
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/dispatcher.html
 @@ -9,15 +9,15 @@
  -->
    <META NAME="keywords" CONTENT="dispatcher toolkit">
@@ -392,8 +392,8 @@ Combined patches from git.
      <!-- right content column  --> 
      <td width="460"> 
        <p>&nbsp;</p>
---- ncbi-tools6-6.1.20170106.orig/doc/firewall.html
-+++ ncbi-tools6-6.1.20170106/doc/firewall.html
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/firewall.html
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/firewall.html
 @@ -9,15 +9,15 @@
   <META NAME="keywords" CONTENT="insert your keywords for the search engine">
   <META NAME="description" CONTENT="insert the description to be displayed by the search engine.  Also searched by the search engine.">
@@ -455,8 +455,8 @@ Combined patches from git.
  the preset ports, and it is kept in-sync with currently
  configured open ports (so remember to refresh your download
  prior to actual use).
---- ncbi-tools6-6.1.20170106.orig/doc/fwd_check.sh
-+++ ncbi-tools6-6.1.20170106/doc/fwd_check.sh
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/fwd_check.sh
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/fwd_check.sh
 @@ -8,7 +8,7 @@
  delay_sec="$1"
  delay_sec=${delay_sec:="10"}
@@ -466,8 +466,8 @@ Combined patches from git.
  helper="./fwd_failure_helper.exe"
  test -z "$netcat"  &&  netcat="`whereis nc | sed 's/^[^:]*://;s/ //g'`"
  test -z "$HTTP_NCBI_EXTERNAL"  &&  HTTP_CAF_EXTERNAL="$HTTP_NCBI_EXTERNAL"
---- ncbi-tools6-6.1.20170106.orig/doc/man/cleanasn.1
-+++ ncbi-tools6-6.1.20170106/doc/man/cleanasn.1
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/man/cleanasn.1
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/man/cleanasn.1
 @@ -1,4 +1,4 @@
 -.TH CLEANASN 1 2016-09-01 NCBI "NCBI Tools User's Manual"
 +.TH CLEANASN 1 2017-01-09 NCBI "NCBI Tools User's Manual"
@@ -495,7 +495,7 @@ Combined patches from git.
  Virtual gaps inside segmented sequence
  .IP s
 --- /dev/null
-+++ ncbi-tools6-6.1.20170106/doc/man/taxblast.1
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/man/taxblast.1
 @@ -0,0 +1,31 @@
 +.TH TAXBLAST 1 2016-12-05 NCBI "NCBI Tools User's Manual"
 +.SH NAME
@@ -528,8 +528,8 @@ Combined patches from git.
 +Sequence is DNA
 +.SH AUTHOR
 +The National Center for Biotechnology Information.
---- ncbi-tools6-6.1.20170106.orig/make/makeall.unx
-+++ ncbi-tools6-6.1.20170106/make/makeall.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makeall.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makeall.unx
 @@ -1,4 +1,4 @@
 -#	makefile for asntool and ncbi core routines,
 +#	-*- makefile -*- for asntool and ncbi core routines,
@@ -597,8 +597,8 @@ Combined patches from git.
  	cp -fp ../algo/blast/composition_adjustment/*.h \
  		../include/algo/blast/composition_adjustment
  	- mkdir -p ../include/algo/blast/api
---- ncbi-tools6-6.1.20170106.orig/make/makedemo.unx
-+++ ncbi-tools6-6.1.20170106/make/makedemo.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makedemo.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makedemo.unx
 @@ -1,4 +1,4 @@
 -#	makefile for demo programs
 +#	-*- makefile -*- for demo programs
@@ -615,8 +615,8 @@ Combined patches from git.
  
  # errhdr
  
---- ncbi-tools6-6.1.20170106.orig/make/makenet.unx
-+++ ncbi-tools6-6.1.20170106/make/makenet.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makenet.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makenet.unx
 @@ -1,4 +1,4 @@
 -#   makefile for network demo programs and network entrez
 +#   -*- makefile -*- for network demo programs and network entrez
@@ -723,8 +723,8 @@ Combined patches from git.
  
  # test client for the suggest network service
  suggcli: suggcli.c $(BNETCLILIB) $(BLIB24)
---- ncbi-tools6-6.1.20170106.orig/make/makeshlb.unx
-+++ ncbi-tools6-6.1.20170106/make/makeshlb.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makeshlb.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makeshlb.unx
 @@ -1,4 +1,4 @@
 -#
 +# -*- makefile -*-
@@ -848,8 +848,8 @@ Combined patches from git.
 +libvibnet.$(so):      $(libvibnet_deps)
 +# libvibrant.$(so):   $(libvibrant_deps)
 +libvibrantOGL.$(so):  $(libvibrantOGL_deps)
---- ncbi-tools6-6.1.20170106.orig/tools/readdb.c
-+++ ncbi-tools6-6.1.20170106/tools/readdb.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/tools/readdb.c
++++ ncbi-tools6-6.1.20170106+dfsg1/tools/readdb.c
 @@ -10167,7 +10167,10 @@ static    Int2    FDBFinish (FormatDBPtr
              return 1;
      
@@ -862,8 +862,8 @@ Combined patches from git.
  
      /* write db_title and date-time stamp eigth bytes aligned */
      tmp = title_len + StringLen(dateTime);
---- ncbi-tools6-6.1.20170106.orig/vibrant/netscape.c
-+++ ncbi-tools6-6.1.20170106/vibrant/netscape.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/netscape.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/netscape.c
 @@ -548,9 +548,8 @@ static Boolean NS_LoadNetscape(const cha
      }
  
@@ -876,8 +876,8 @@ Combined patches from git.
          exit(1);
      }
  
---- ncbi-tools6-6.1.20170106.orig/vibrant/shim3d.c
-+++ ncbi-tools6-6.1.20170106/vibrant/shim3d.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/shim3d.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/shim3d.c
 @@ -321,6 +321,7 @@
  
  #ifdef _PNG
@@ -918,8 +918,8 @@ Combined patches from git.
          MemFree(fblock);
  }
 -
---- ncbi-tools6-6.1.20170106.orig/vibrant/vibmain.c
-+++ ncbi-tools6-6.1.20170106/vibrant/vibmain.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/vibmain.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/vibmain.c
 @@ -44,6 +44,21 @@
  
  
@@ -942,8 +942,8 @@ Combined patches from git.
  #ifdef WIN_MAC
  #ifdef OS_UNIX_DARWIN
  int main (int argc, char *argv[]) 
---- ncbi-tools6-6.1.20170106.orig/vibrant/vibwndws.c
-+++ ncbi-tools6-6.1.20170106/vibrant/vibwndws.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/vibwndws.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/vibwndws.c
 @@ -6818,7 +6818,7 @@ extern void Nlm_VibMainPrelude (int argc
    Nlm_InitPrompt ();
    Nlm_InitSlate ();